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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2023-05-14, 19:01 CEST based on data in:

        General Statistics

        Showing 414/414 rows and 4/6 columns.
        Sample Name% Dups% GCMedian Read LengthM Seqs
        SAMEA1964687_1
        11.7%
        48%
        90 bp
        33.8
        SAMEA1964687_2
        11.1%
        48%
        90 bp
        33.8
        SAMEA1964695_1
        11.9%
        43%
        73 bp
        28.5
        SAMEA1964695_2
        11.2%
        43%
        75 bp
        28.5
        SAMEA1964852_1
        8.9%
        44%
        75 bp
        32.0
        SAMEA1964852_2
        5.9%
        44%
        75 bp
        32.0
        SAMEA1965149_1
        8.4%
        48%
        90 bp
        48.9
        SAMEA1965149_2
        7.6%
        48%
        90 bp
        48.9
        SAMEA1965858_1
        20.9%
        46%
        90 bp
        58.9
        SAMEA1965858_2
        19.2%
        46%
        90 bp
        58.9
        SAMEA1966821_1
        6.3%
        44%
        73 bp
        29.5
        SAMEA1966821_2
        5.7%
        44%
        75 bp
        29.5
        SAMEA1967319_1
        33.6%
        45%
        90 bp
        38.7
        SAMEA1967319_2
        31.4%
        45%
        90 bp
        38.7
        SAMEA1967891_1
        16.3%
        46%
        75 bp
        30.4
        SAMEA1967891_2
        0.2%
        46%
        75 bp
        30.4
        SAMEA1969126_1
        9.3%
        46%
        73 bp
        29.4
        SAMEA1969126_2
        8.0%
        46%
        75 bp
        29.4
        SAMEA1969178_1
        7.7%
        44%
        75 bp
        29.4
        SAMEA1969178_2
        6.9%
        45%
        75 bp
        29.4
        SAMEA1969417_1
        27.5%
        47%
        90 bp
        32.6
        SAMEA1969417_2
        25.5%
        47%
        90 bp
        32.6
        SAMEA1970858_1
        13.6%
        49%
        90 bp
        43.4
        SAMEA1970858_2
        12.6%
        50%
        90 bp
        43.4
        SAMEA1971210_1
        20.7%
        47%
        90 bp
        44.8
        SAMEA1971210_2
        19.1%
        47%
        90 bp
        44.8
        SAMEA1972188_1
        29.4%
        46%
        90 bp
        53.9
        SAMEA1972188_2
        27.7%
        46%
        90 bp
        53.9
        SAMEA1972381_1
        9.9%
        47%
        90 bp
        43.5
        SAMEA1972381_2
        9.1%
        47%
        90 bp
        43.5
        SAMEA2142349_1
        9.8%
        48%
        90 bp
        49.3
        SAMEA2142349_2
        8.9%
        48%
        90 bp
        49.3
        SAMEA2142525_1
        24.8%
        43%
        75 bp
        37.2
        SAMEA2142525_2
        22.6%
        43%
        75 bp
        37.2
        SAMEA2142594_1
        6.4%
        43%
        75 bp
        32.8
        SAMEA2142594_2
        0.1%
        43%
        75 bp
        32.8
        SAMEA2142793_1
        19.2%
        44%
        75 bp
        37.2
        SAMEA2142793_2
        17.6%
        44%
        75 bp
        37.2
        SAMEA2142846_1
        7.4%
        45%
        73 bp
        29.6
        SAMEA2142846_2
        5.0%
        46%
        75 bp
        29.6
        SAMEA2142848_1
        10.7%
        45%
        73 bp
        29.6
        SAMEA2142848_2
        9.6%
        45%
        75 bp
        29.6
        SAMEA2142970_1
        9.8%
        46%
        90 bp
        43.8
        SAMEA2142970_2
        8.7%
        46%
        90 bp
        43.8
        SAMEA2143074_1
        20.4%
        46%
        90 bp
        51.9
        SAMEA2143074_2
        19.0%
        46%
        90 bp
        51.9
        SAMEA2143633_1
        12.3%
        48%
        90 bp
        45.4
        SAMEA2143633_2
        11.7%
        48%
        90 bp
        45.4
        SAMEA2143863_1
        11.3%
        48%
        90 bp
        40.4
        SAMEA2143863_2
        10.1%
        48%
        90 bp
        40.4
        SAMEA2143980_1
        8.2%
        47%
        75 bp
        29.7
        SAMEA2143980_2
        4.8%
        49%
        75 bp
        29.7
        SAMEA2144223_1
        25.0%
        47%
        90 bp
        46.2
        SAMEA2144223_2
        22.3%
        47%
        90 bp
        46.2
        SAMEA2144304_1
        12.1%
        48%
        90 bp
        44.3
        SAMEA2144304_2
        10.8%
        48%
        90 bp
        44.3
        SAMEA2144396_1
        6.6%
        48%
        90 bp
        37.7
        SAMEA2144396_2
        6.0%
        48%
        90 bp
        37.7
        SAMEA2144525_1
        11.5%
        43%
        73 bp
        28.3
        SAMEA2144525_2
        10.4%
        43%
        75 bp
        28.3
        SAMEA2144555_1
        11.9%
        49%
        90 bp
        49.4
        SAMEA2144555_2
        10.6%
        49%
        90 bp
        49.4
        SAMEA2144578_1
        20.0%
        43%
        73 bp
        30.0
        SAMEA2144578_2
        18.4%
        44%
        75 bp
        30.0
        SAMEA2144588_1
        10.9%
        45%
        73 bp
        39.0
        SAMEA2144588_2
        10.2%
        46%
        75 bp
        39.0
        SAMEA2144623_1
        12.7%
        44%
        75 bp
        36.9
        SAMEA2144623_2
        11.5%
        44%
        75 bp
        36.9
        SAMEA2144980_1
        22.6%
        47%
        90 bp
        44.4
        SAMEA2144980_2
        20.9%
        47%
        90 bp
        44.4
        SAMEA2145068_1
        10.3%
        43%
        73 bp
        29.4
        SAMEA2145068_2
        9.8%
        43%
        75 bp
        29.4
        SAMEA2145301_1
        13.3%
        43%
        75 bp
        35.9
        SAMEA2145301_2
        12.3%
        43%
        75 bp
        35.9
        SAMEA2145365_1
        8.9%
        46%
        90 bp
        48.0
        SAMEA2145365_2
        7.8%
        46%
        90 bp
        48.0
        SAMEA2145582_1
        7.5%
        47%
        75 bp
        29.8
        SAMEA2145582_2
        5.3%
        47%
        75 bp
        29.8
        SAMEA2145648_1
        18.8%
        44%
        75 bp
        29.8
        SAMEA2145648_2
        11.0%
        45%
        75 bp
        29.8
        SAMEA2145758_1
        11.4%
        44%
        73 bp
        29.6
        SAMEA2145758_2
        10.3%
        44%
        75 bp
        29.6
        SAMEA2145815_1
        8.3%
        46%
        90 bp
        39.5
        SAMEA2145815_2
        7.4%
        46%
        90 bp
        39.5
        SAMEA2146009_1
        15.7%
        47%
        90 bp
        45.9
        SAMEA2146009_2
        13.6%
        47%
        90 bp
        45.9
        SAMEA2146107_1
        8.4%
        51%
        90 bp
        38.3
        SAMEA2146107_2
        7.1%
        51%
        90 bp
        38.3
        SAMEA2146320_1
        7.4%
        43%
        73 bp
        31.0
        SAMEA2146320_2
        6.2%
        43%
        75 bp
        31.0
        SAMEA2146477_1
        9.2%
        48%
        90 bp
        47.8
        SAMEA2146477_2
        8.0%
        48%
        90 bp
        47.8
        SAMEA2146552_1
        16.3%
        48%
        90 bp
        52.4
        SAMEA2146552_2
        15.1%
        48%
        90 bp
        52.4
        SAMEA2146600_1
        15.5%
        45%
        90 bp
        38.6
        SAMEA2146600_2
        14.7%
        45%
        90 bp
        38.6
        SAMEA2146682_1
        4.3%
        44%
        73 bp
        35.7
        SAMEA2146682_2
        3.8%
        45%
        75 bp
        35.7
        SAMEA2146731_1
        9.7%
        44%
        73 bp
        33.3
        SAMEA2146731_2
        9.1%
        44%
        75 bp
        33.3
        SAMEA2146908_1
        9.8%
        43%
        73 bp
        27.5
        SAMEA2146908_2
        8.6%
        43%
        75 bp
        27.5
        SAMEA2147022_1
        17.7%
        43%
        73 bp
        33.0
        SAMEA2147022_2
        16.4%
        43%
        75 bp
        33.0
        SAMEA2147036_1
        21.8%
        46%
        90 bp
        43.0
        SAMEA2147036_2
        19.8%
        46%
        90 bp
        43.0
        SAMEA2147070_1
        7.9%
        45%
        73 bp
        30.2
        SAMEA2147070_2
        7.0%
        45%
        75 bp
        30.2
        SAMEA2147092_1
        18.2%
        42%
        75 bp
        29.7
        SAMEA2147092_2
        11.9%
        43%
        75 bp
        29.7
        SAMEA2147114_1
        11.9%
        44%
        75 bp
        35.4
        SAMEA2147114_2
        10.3%
        44%
        75 bp
        35.4
        SAMEA2147216_1
        16.0%
        44%
        73 bp
        31.8
        SAMEA2147216_2
        15.1%
        45%
        75 bp
        31.8
        SAMEA2147326_1
        22.5%
        44%
        90 bp
        44.6
        SAMEA2147326_2
        21.1%
        44%
        90 bp
        44.6
        SAMEA2147384_1
        17.4%
        42%
        73 bp
        30.8
        SAMEA2147384_2
        16.2%
        43%
        75 bp
        30.8
        SAMEA2147587_1
        12.0%
        43%
        75 bp
        35.2
        SAMEA2147587_2
        9.4%
        44%
        75 bp
        35.2
        SAMEA2147589_1
        23.5%
        43%
        73 bp
        31.6
        SAMEA2147589_2
        21.0%
        43%
        75 bp
        31.6
        SAMEA2147991_1
        17.1%
        44%
        75 bp
        34.9
        SAMEA2147991_2
        16.0%
        44%
        75 bp
        34.9
        SAMEA2148094_1
        17.2%
        48%
        90 bp
        53.2
        SAMEA2148094_2
        16.1%
        48%
        90 bp
        53.2
        SAMEA2148105_1
        37.9%
        44%
        73 bp
        31.5
        SAMEA2148105_2
        35.4%
        45%
        75 bp
        31.5
        SAMEA2148265_1
        14.3%
        45%
        75 bp
        29.7
        SAMEA2148265_2
        10.6%
        46%
        75 bp
        29.7
        SAMEA2148412_1
        9.3%
        47%
        90 bp
        46.0
        SAMEA2148412_2
        8.6%
        47%
        90 bp
        46.0
        SAMEA2148549_1
        7.6%
        46%
        75 bp
        29.2
        SAMEA2148549_2
        2.5%
        48%
        75 bp
        29.2
        SAMEA2148755_1
        12.8%
        46%
        90 bp
        43.8
        SAMEA2148755_2
        12.1%
        46%
        90 bp
        43.8
        SAMEA2149068_1
        23.4%
        45%
        90 bp
        49.4
        SAMEA2149068_2
        21.8%
        45%
        90 bp
        49.4
        SAMEA2149228_1
        15.1%
        46%
        90 bp
        40.2
        SAMEA2149228_2
        13.2%
        46%
        90 bp
        40.2
        SAMEA2149241_1
        18.8%
        46%
        90 bp
        49.0
        SAMEA2149241_2
        17.4%
        46%
        90 bp
        49.0
        SAMEA2149271_1
        17.4%
        47%
        90 bp
        33.3
        SAMEA2149271_2
        17.0%
        47%
        90 bp
        33.3
        SAMEA2149539_1
        11.7%
        43%
        73 bp
        40.4
        SAMEA2149539_2
        8.5%
        43%
        75 bp
        40.4
        SAMEA2149636_1
        15.4%
        46%
        90 bp
        53.4
        SAMEA2149636_2
        13.9%
        47%
        90 bp
        53.4
        SAMEA2149794_1
        31.5%
        47%
        90 bp
        45.1
        SAMEA2149794_2
        28.8%
        47%
        90 bp
        45.1
        SAMEA2149983_1
        13.4%
        47%
        90 bp
        44.1
        SAMEA2149983_2
        12.6%
        47%
        90 bp
        44.1
        SAMEA2150168_1
        20.3%
        45%
        90 bp
        52.3
        SAMEA2150168_2
        19.8%
        45%
        90 bp
        52.3
        SAMEA2150234_1
        18.3%
        48%
        90 bp
        45.6
        SAMEA2150234_2
        16.5%
        48%
        90 bp
        45.6
        SAMEA2150447_1
        7.4%
        47%
        75 bp
        29.4
        SAMEA2150447_2
        3.4%
        49%
        75 bp
        29.4
        SAMEA2150563_1
        10.1%
        47%
        90 bp
        31.0
        SAMEA2150563_2
        9.7%
        48%
        90 bp
        31.0
        SAMEA2150726_1
        8.2%
        49%
        90 bp
        49.6
        SAMEA2150726_2
        7.2%
        49%
        90 bp
        49.6
        SAMEA2150876_1
        16.2%
        45%
        73 bp
        31.2
        SAMEA2150876_2
        14.7%
        46%
        75 bp
        31.2
        SAMEA2150909_1
        9.3%
        45%
        73 bp
        29.2
        SAMEA2150909_2
        8.4%
        46%
        75 bp
        29.2
        SAMEA2151007_1
        8.2%
        47%
        90 bp
        39.7
        SAMEA2151007_2
        7.5%
        47%
        90 bp
        39.7
        SAMEA2151010_1
        15.3%
        47%
        90 bp
        48.4
        SAMEA2151010_2
        14.4%
        47%
        90 bp
        48.4
        SAMEA2151034_1
        16.6%
        44%
        75 bp
        33.9
        SAMEA2151034_2
        14.3%
        44%
        75 bp
        33.9
        SAMEA2151383_1
        14.9%
        50%
        90 bp
        47.7
        SAMEA2151383_2
        13.3%
        50%
        90 bp
        47.7
        SAMEA2151391_1
        11.0%
        43%
        73 bp
        37.8
        SAMEA2151391_2
        9.8%
        43%
        75 bp
        37.8
        SAMEA2151439_1
        15.9%
        49%
        90 bp
        38.1
        SAMEA2151439_2
        14.8%
        49%
        90 bp
        38.1
        SAMEA2151606_1
        6.8%
        46%
        73 bp
        27.3
        SAMEA2151606_2
        5.8%
        46%
        75 bp
        27.3
        SAMEA2151633_1
        25.7%
        48%
        90 bp
        36.8
        SAMEA2151633_2
        23.3%
        48%
        90 bp
        36.8
        SAMEA2151677_1
        3.9%
        45%
        73 bp
        27.7
        SAMEA2151677_2
        3.8%
        45%
        75 bp
        27.7
        SAMEA2151703_1
        17.7%
        46%
        90 bp
        44.3
        SAMEA2151703_2
        16.2%
        47%
        90 bp
        44.3
        SAMEA2151838_1
        14.8%
        47%
        75 bp
        31.1
        SAMEA2151838_2
        13.4%
        47%
        75 bp
        31.1
        SAMEA2152063_1
        24.4%
        47%
        90 bp
        44.4
        SAMEA2152063_2
        22.4%
        47%
        90 bp
        44.4
        SAMEA2152064_1
        9.4%
        50%
        90 bp
        49.4
        SAMEA2152064_2
        8.9%
        50%
        90 bp
        49.4
        SAMEA2152065_1
        3.6%
        46%
        73 bp
        28.4
        SAMEA2152065_2
        3.1%
        46%
        75 bp
        28.4
        SAMEA2152125_1
        10.5%
        43%
        75 bp
        33.1
        SAMEA2152125_2
        9.9%
        43%
        75 bp
        33.1
        SAMEA2152204_1
        20.7%
        42%
        75 bp
        28.8
        SAMEA2152204_2
        17.8%
        43%
        75 bp
        28.8
        SAMEA2152373_1
        12.2%
        51%
        90 bp
        46.5
        SAMEA2152373_2
        10.7%
        51%
        90 bp
        46.5
        SAMEA2152443_1
        12.2%
        47%
        90 bp
        46.7
        SAMEA2152443_2
        10.3%
        47%
        90 bp
        46.7
        SAMEA2152521_1
        9.6%
        46%
        90 bp
        42.5
        SAMEA2152521_2
        8.8%
        46%
        90 bp
        42.5
        SAMEA2152531_1
        13.6%
        45%
        90 bp
        47.2
        SAMEA2152531_2
        11.7%
        46%
        90 bp
        47.2
        SAMEA2152591_1
        20.3%
        46%
        90 bp
        57.8
        SAMEA2152591_2
        18.2%
        46%
        90 bp
        57.8
        SAMEA2152938_1
        9.9%
        49%
        90 bp
        35.5
        SAMEA2152938_2
        9.0%
        49%
        90 bp
        35.5
        SAMEA2153005_1
        30.0%
        48%
        90 bp
        44.5
        SAMEA2153005_2
        28.3%
        48%
        90 bp
        44.5
        SAMEA2153010_1
        12.1%
        44%
        73 bp
        30.6
        SAMEA2153010_2
        10.7%
        44%
        75 bp
        30.6
        SAMEA2153251_1
        18.7%
        45%
        90 bp
        40.1
        SAMEA2153251_2
        17.0%
        45%
        90 bp
        40.1
        SAMEA2153397_1
        12.4%
        46%
        90 bp
        48.4
        SAMEA2153397_2
        11.1%
        46%
        90 bp
        48.4
        SAMEA2153557_1
        15.4%
        44%
        73 bp
        40.9
        SAMEA2153557_2
        15.8%
        44%
        75 bp
        40.9
        SAMEA2153852_1
        9.9%
        48%
        90 bp
        51.4
        SAMEA2153852_2
        9.3%
        48%
        90 bp
        51.4
        SAMEA2153898_1
        53.7%
        49%
        90 bp
        53.7
        SAMEA2153898_2
        51.8%
        49%
        90 bp
        53.7
        SAMEA2154015_1
        11.2%
        49%
        90 bp
        51.9
        SAMEA2154015_2
        9.7%
        49%
        90 bp
        51.9
        SAMEA2154036_1
        17.7%
        44%
        90 bp
        42.9
        SAMEA2154036_2
        16.1%
        44%
        90 bp
        42.9
        SAMEA2154047_1
        8.7%
        44%
        75 bp
        32.7
        SAMEA2154047_2
        8.7%
        45%
        75 bp
        32.7
        SAMEA2154150_1
        19.9%
        45%
        90 bp
        50.2
        SAMEA2154150_2
        18.3%
        45%
        90 bp
        50.2
        SAMEA2154452_1
        5.9%
        45%
        73 bp
        30.0
        SAMEA2154452_2
        5.1%
        46%
        75 bp
        30.0
        SAMEA2154516_1
        32.7%
        46%
        90 bp
        31.7
        SAMEA2154516_2
        32.0%
        46%
        90 bp
        31.7
        SAMEA2154561_1
        12.7%
        47%
        90 bp
        45.8
        SAMEA2154561_2
        11.6%
        47%
        90 bp
        45.8
        SAMEA2154620_1
        7.1%
        48%
        90 bp
        44.6
        SAMEA2154620_2
        6.7%
        48%
        90 bp
        44.6
        SAMEA2154893_1
        15.9%
        44%
        73 bp
        27.8
        SAMEA2154893_2
        13.7%
        44%
        75 bp
        27.8
        SAMEA2154920_1
        20.3%
        44%
        73 bp
        29.3
        SAMEA2154920_2
        17.7%
        44%
        75 bp
        29.3
        SAMEA2154992_1
        7.2%
        44%
        73 bp
        31.2
        SAMEA2154992_2
        6.6%
        44%
        75 bp
        31.2
        SAMEA2155093_1
        30.1%
        47%
        90 bp
        41.2
        SAMEA2155093_2
        27.8%
        47%
        90 bp
        41.2
        SAMEA2155134_1
        9.0%
        46%
        90 bp
        47.2
        SAMEA2155134_2
        8.2%
        46%
        90 bp
        47.2
        SAMEA2155255_1
        7.7%
        49%
        90 bp
        45.1
        SAMEA2155255_2
        7.0%
        49%
        90 bp
        45.1
        SAMEA2155310_1
        8.2%
        44%
        73 bp
        34.2
        SAMEA2155310_2
        7.6%
        44%
        75 bp
        34.2
        SAMEA2155373_1
        8.3%
        44%
        73 bp
        31.6
        SAMEA2155373_2
        7.2%
        45%
        75 bp
        31.6
        SAMEA2155512_1
        18.7%
        46%
        90 bp
        49.9
        SAMEA2155512_2
        16.8%
        46%
        90 bp
        49.9
        SAMEA2155520_1
        13.5%
        46%
        90 bp
        40.6
        SAMEA2155520_2
        11.7%
        46%
        90 bp
        40.6
        SAMEA2155636_1
        6.9%
        46%
        73 bp
        29.1
        SAMEA2155636_2
        6.0%
        46%
        75 bp
        29.1
        SAMEA2155689_1
        14.3%
        43%
        75 bp
        32.1
        SAMEA2155689_2
        11.5%
        43%
        75 bp
        32.1
        SAMEA2155758_1
        8.7%
        49%
        90 bp
        42.3
        SAMEA2155758_2
        7.9%
        49%
        90 bp
        42.3
        SAMEA2155902_1
        18.5%
        48%
        90 bp
        46.5
        SAMEA2155902_2
        17.1%
        48%
        90 bp
        46.5
        SAMEA2156032_1
        28.9%
        48%
        90 bp
        46.1
        SAMEA2156032_2
        27.1%
        49%
        90 bp
        46.1
        SAMEA2156362_1
        12.3%
        44%
        73 bp
        30.0
        SAMEA2156362_2
        7.7%
        45%
        75 bp
        30.0
        SAMEA2156486_1
        7.3%
        47%
        90 bp
        47.6
        SAMEA2156486_2
        6.9%
        47%
        90 bp
        47.6
        SAMEA2156577_1
        12.4%
        48%
        90 bp
        36.0
        SAMEA2156577_2
        11.3%
        48%
        90 bp
        36.0
        SAMEA2156675_1
        11.7%
        47%
        75 bp
        33.5
        SAMEA2156675_2
        10.7%
        47%
        75 bp
        33.5
        SAMEA2156714_1
        12.1%
        48%
        90 bp
        46.6
        SAMEA2156714_2
        10.6%
        48%
        90 bp
        46.6
        SAMEA2156850_1
        10.6%
        48%
        90 bp
        48.2
        SAMEA2156850_2
        9.8%
        48%
        90 bp
        48.2
        SAMEA2156906_1
        18.2%
        47%
        73 bp
        30.7
        SAMEA2156906_2
        16.0%
        48%
        75 bp
        30.7
        SAMEA2157028_1
        17.1%
        42%
        75 bp
        38.3
        SAMEA2157028_2
        15.9%
        43%
        75 bp
        38.3
        SAMEA2157192_1
        10.2%
        45%
        73 bp
        27.6
        SAMEA2157192_2
        9.5%
        45%
        75 bp
        27.6
        SAMEA2157273_1
        13.2%
        43%
        75 bp
        33.4
        SAMEA2157273_2
        11.9%
        43%
        75 bp
        33.4
        SAMEA2157747_1
        15.2%
        44%
        75 bp
        33.3
        SAMEA2157747_2
        14.5%
        44%
        75 bp
        33.3
        SAMEA2157793_1
        8.2%
        46%
        75 bp
        28.2
        SAMEA2157793_2
        4.6%
        48%
        75 bp
        28.2
        SAMEA2157850_1
        14.6%
        47%
        90 bp
        53.7
        SAMEA2157850_2
        13.5%
        48%
        90 bp
        53.7
        SAMEA2157909_1
        25.8%
        45%
        73 bp
        30.2
        SAMEA2157909_2
        23.5%
        45%
        75 bp
        30.2
        SAMEA2157917_1
        13.1%
        49%
        90 bp
        41.8
        SAMEA2157917_2
        12.6%
        49%
        90 bp
        41.8
        SAMEA2157972_1
        9.1%
        48%
        90 bp
        54.6
        SAMEA2157972_2
        8.3%
        48%
        90 bp
        54.6
        SAMEA2157977_1
        10.8%
        48%
        90 bp
        32.4
        SAMEA2157977_2
        9.8%
        48%
        90 bp
        32.4
        SAMEA2158039_1
        10.8%
        48%
        90 bp
        43.6
        SAMEA2158039_2
        9.8%
        48%
        90 bp
        43.6
        SAMEA2158062_1
        10.4%
        48%
        90 bp
        49.9
        SAMEA2158062_2
        10.1%
        48%
        90 bp
        49.9
        SAMEA2158100_1
        6.6%
        45%
        73 bp
        27.8
        SAMEA2158100_2
        5.9%
        45%
        75 bp
        27.8
        SAMEA2158190_1
        13.9%
        49%
        90 bp
        38.0
        SAMEA2158190_2
        12.4%
        49%
        90 bp
        38.0
        SAMEA2158269_1
        18.3%
        44%
        75 bp
        35.0
        SAMEA2158269_2
        16.0%
        44%
        75 bp
        35.0
        SAMEA2158408_1
        16.2%
        43%
        73 bp
        32.9
        SAMEA2158408_2
        11.8%
        43%
        75 bp
        32.9
        SAMEA2158454_1
        6.9%
        44%
        73 bp
        29.1
        SAMEA2158454_2
        6.2%
        44%
        75 bp
        29.1
        SAMEA2158468_1
        8.6%
        48%
        90 bp
        46.7
        SAMEA2158468_2
        7.8%
        48%
        90 bp
        46.7
        SAMEA2158521_1
        6.7%
        45%
        73 bp
        27.6
        SAMEA2158521_2
        6.0%
        46%
        75 bp
        27.6
        SAMEA2158542_1
        8.5%
        48%
        90 bp
        44.3
        SAMEA2158542_2
        7.4%
        49%
        90 bp
        44.3
        SAMEA2158769_1
        11.4%
        49%
        90 bp
        47.7
        SAMEA2158769_2
        9.6%
        49%
        90 bp
        47.7
        SAMEA2159032_1
        11.3%
        46%
        90 bp
        44.1
        SAMEA2159032_2
        10.1%
        46%
        90 bp
        44.1
        SAMEA2159102_1
        10.8%
        49%
        90 bp
        30.6
        SAMEA2159102_2
        10.3%
        49%
        90 bp
        30.6
        SAMEA2159162_1
        14.0%
        46%
        90 bp
        46.7
        SAMEA2159162_2
        12.8%
        46%
        90 bp
        46.7
        SAMEA2159202_1
        17.8%
        47%
        90 bp
        33.6
        SAMEA2159202_2
        16.3%
        47%
        90 bp
        33.6
        SAMEA2159338_1
        7.6%
        48%
        90 bp
        32.4
        SAMEA2159338_2
        6.7%
        48%
        90 bp
        32.4
        SAMEA2159408_1
        13.9%
        41%
        75 bp
        35.2
        SAMEA2159408_2
        12.8%
        41%
        75 bp
        35.2
        SAMEA2159429_1
        11.2%
        46%
        73 bp
        41.9
        SAMEA2159429_2
        10.2%
        46%
        75 bp
        41.9
        SAMEA2159529_1
        14.8%
        46%
        90 bp
        43.2
        SAMEA2159529_2
        13.5%
        46%
        90 bp
        43.2
        SAMEA2159561_1
        24.3%
        44%
        75 bp
        33.2
        SAMEA2159561_2
        22.3%
        44%
        75 bp
        33.2
        SAMEA2159881_1
        10.5%
        50%
        90 bp
        46.4
        SAMEA2159881_2
        9.3%
        50%
        90 bp
        46.4
        SAMEA2159891_1
        8.3%
        43%
        75 bp
        29.8
        SAMEA2159891_2
        0.0%
        43%
        75 bp
        29.8
        SAMEA2159974_1
        10.4%
        49%
        90 bp
        37.9
        SAMEA2159974_2
        9.7%
        49%
        90 bp
        37.9
        SAMEA2160045_1
        6.0%
        46%
        73 bp
        29.7
        SAMEA2160045_2
        5.1%
        46%
        75 bp
        29.7
        SAMEA2160152_1
        25.1%
        46%
        90 bp
        51.2
        SAMEA2160152_2
        23.1%
        46%
        90 bp
        51.2
        SAMEA2160437_1
        3.5%
        46%
        73 bp
        27.5
        SAMEA2160437_2
        1.8%
        46%
        75 bp
        27.5
        SAMEA2160490_1
        10.9%
        48%
        90 bp
        46.4
        SAMEA2160490_2
        9.7%
        48%
        90 bp
        46.4
        SAMEA2160616_1
        6.6%
        49%
        90 bp
        40.0
        SAMEA2160616_2
        5.9%
        49%
        90 bp
        40.0
        SAMEA2160902_1
        29.7%
        44%
        90 bp
        35.8
        SAMEA2160902_2
        27.6%
        45%
        90 bp
        35.8
        SAMEA2160998_1
        10.4%
        48%
        90 bp
        45.1
        SAMEA2160998_2
        9.4%
        48%
        90 bp
        45.1
        SAMEA2161021_1
        17.0%
        41%
        75 bp
        31.8
        SAMEA2161021_2
        14.2%
        42%
        75 bp
        31.8
        SAMEA2161222_1
        15.3%
        42%
        75 bp
        32.4
        SAMEA2161222_2
        14.1%
        43%
        75 bp
        32.4
        SAMEA2161311_1
        15.3%
        47%
        90 bp
        50.2
        SAMEA2161311_2
        12.9%
        47%
        90 bp
        50.2
        SAMEA2161372_1
        17.7%
        45%
        90 bp
        58.5
        SAMEA2161372_2
        16.3%
        45%
        90 bp
        58.5
        SAMEA2161597_1
        11.8%
        51%
        90 bp
        44.5
        SAMEA2161597_2
        10.3%
        51%
        90 bp
        44.5
        SAMEA2161657_1
        14.4%
        46%
        90 bp
        37.8
        SAMEA2161657_2
        13.2%
        46%
        90 bp
        37.8
        SAMEA2161897_1
        32.2%
        45%
        90 bp
        58.9
        SAMEA2161897_2
        31.5%
        45%
        90 bp
        58.9
        SAMEA2162036_1
        7.6%
        47%
        90 bp
        43.0
        SAMEA2162036_2
        6.9%
        47%
        90 bp
        43.0
        SAMEA2162182_1
        8.8%
        45%
        75 bp
        34.3
        SAMEA2162182_2
        8.3%
        45%
        75 bp
        34.3
        SAMEA2162200_1
        7.9%
        44%
        73 bp
        26.5
        SAMEA2162200_2
        8.2%
        44%
        75 bp
        26.5
        SAMEA2162231_1
        17.1%
        42%
        75 bp
        30.8
        SAMEA2162231_2
        15.1%
        42%
        75 bp
        30.8
        SAMEA2162259_1
        10.5%
        44%
        73 bp
        26.3
        SAMEA2162259_2
        8.7%
        45%
        75 bp
        26.3
        SAMEA2162475_1
        16.0%
        46%
        90 bp
        48.7
        SAMEA2162475_2
        15.1%
        46%
        90 bp
        48.7
        SAMEA2162573_1
        36.2%
        47%
        90 bp
        44.9
        SAMEA2162573_2
        33.1%
        47%
        90 bp
        44.9
        SAMEA2162640_1
        15.9%
        46%
        90 bp
        49.0
        SAMEA2162640_2
        15.0%
        46%
        90 bp
        49.0
        SAMEA2162811_1
        14.2%
        47%
        90 bp
        50.8
        SAMEA2162811_2
        12.8%
        47%
        90 bp
        50.8
        SAMEA2162844_1
        14.7%
        46%
        90 bp
        46.3
        SAMEA2162844_2
        13.5%
        46%
        90 bp
        46.3
        SAMEA2162862_1
        8.2%
        47%
        75 bp
        30.6
        SAMEA2162862_2
        6.3%
        47%
        75 bp
        30.6
        SAMEA2162880_1
        20.6%
        43%
        73 bp
        31.9
        SAMEA2162880_2
        12.4%
        43%
        75 bp
        31.9
        SAMEA2163248_1
        5.3%
        44%
        73 bp
        27.6
        SAMEA2163248_2
        5.1%
        44%
        75 bp
        27.6
        SAMEA2163351_1
        15.6%
        44%
        73 bp
        30.6
        SAMEA2163351_2
        12.8%
        44%
        75 bp
        30.6
        SAMEA2163432_1
        12.7%
        50%
        90 bp
        58.5
        SAMEA2163432_2
        11.8%
        50%
        90 bp
        58.5
        SAMEA2163504_1
        11.3%
        45%
        73 bp
        29.4
        SAMEA2163504_2
        10.6%
        45%
        75 bp
        29.4
        SAMEA2163575_1
        9.5%
        43%
        75 bp
        34.0
        SAMEA2163575_2
        8.7%
        43%
        75 bp
        34.0
        SAMEA2163583_1
        10.0%
        48%
        90 bp
        46.0
        SAMEA2163583_2
        9.3%
        48%
        90 bp
        46.0

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        loading..

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        loading..

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        loading..

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        loading..

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        loading..

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        loading..

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        loading..

        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        414 samples had less than 1% of reads made up of overrepresented sequences

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

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        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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        MultiQC v1.14 - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.